After successfully teleporting into the Institute, the Sole Survivor will be greeted by a voice coming from hidden speakers. It's possible to acquire the holotape needed for Inside Job at this point, as the console is right at the entry/exit point of the Institute. After following the voice through the empty Institute corridors and into an elevator, the Sole Survivor eventually enters a room and finds what looks like their son Shaun in a cell, who is acting scared and confused when the Sole Survivor talks to him. Shaun turns out to be a Synth (Synth Shaun) when a man named Father enters the room and shuts him down with a code phrase. He will then initiate conversation with the Sole Survivor. This conversation reveals that he is your son Shaun and the director of the Institute, as well as several other details regarding the Sole Survivor's situation and the details surrounding his initial kidnapping by the Institute. After speaking with him and agreeing to join the Institute (alternatively stalling by telling him they want to think about it), the player character is free to explore the facility.

It is possible to get locked out of the entire Institute questline before it even actually starts. To do so, follow a path of denial and hostility during the meeting with Father, culminating in telling him that you want out or that there's nothing to talk about. He will express regret and will ask you to leave the Institute, which at that point also becomes your new quest objective. Simply retrace your steps back to the two elevators and step into the Relay room where you arrived. You will then be teleported to the C.I.T. ruins, unable to return, and the next main quest for the faction that helped you build Virgil's design will begin instead. Note that this also precludes the player from finishing the game with the Railroad since both questlines are tied together.

If Dr. Madison Li is convinced to leave before completing the objective to meet her, the Sole Survivor will be unable to continue, as the previous dialogue options will not show up.

If you kill Father while being a member in the Railroad, a dramatic change in quests will occur.

If you kill Father right after meeting him, and download the data onto the network scanner, you will be locked out of the Institute and your only choice will be to work with the Minutemen.

pc Dr. Madison Li may not start conversation with the Sole Survivor. This can be fixed by forcing the quest to the next stage (setstage mq207 200), which will then grant you fast travel access and start the next quest. The same can happen to other staff members. For PS4 and Xbox One, reloading a previous save and trying to initiate dialogue again with the Doctor may help fix this. [verification overdue]

pc Father sometimes never shows up. On PC you can use the console (5c337.moveto player) to move Father to your position. The script is waiting for you to talk to the child - so you don't really need to use the console code. [verification overdue]

xboxoneps4 You will not be able to speak to the child if you are wearing a power armor helmet with the mod that highlights lifeforms red. Go back to an earlier save, remove that mod or item, and the scenario should run normally. [verification overdue]

xboxoneps4 Also Clayton Holdren will not be able to speak to you for some reason. Maybe because you went somewhere else while you were supposed to meet him. He shows up on the pip-boy HUD as being in the Synth Retention Bay, but his location is not reachable.[verification overdue]

xboxone When you finish the goal of "speak with the department heads", and the notification comes up on screen that you may now fast travel to and from the institute, the game freezes and crashes.[verification overdue]

ps4 If an unnamed NPC is killed after the Sole Survivor talks to Father, but hasn't officially agreed to join yet by choosing the "Don't Know" option, the quest updates to "Exit the Institute" however it becomes impossible to leave. Furthermore, the quest will not update should the Sole Survivor change their mind and tell Shawn they will join.[verified]

This can be fixed by killing a named NPC and becoming officially banished from the Institute. Otherwise, an earlier save must be reloaded.